Closed:Snakemake, config .yaml

Question

[arshil]

Hi Everyone, can anyone help me with the error i am getting for the config file for snakemake

Config file is not valid JSON or YAML. In case of YAML, make sure to not mix whitespace and tab indentation.

My config file looks like this

RNA_Seqdir: /sfs/qumulo/qproject/CPHG/MILLER/CAD_QTL/coronary_QTL/expression
ref_dir: /scratch/mk9uc/Reference_genomes

#tools and software 
tools:
    fastq: fastqc
    star: STAR
    trimgalore: trim_galore
    featurecount: featureCounts
    rsem:
        exp: rsem-calculate-expression
        ref: rsem-prepare-reference
    RNA_SeqC:
        RNA-SeQC:java -jar RNA-SeQC.jar


# refernce files and genome indces
reference:
    stargenome:
        hg38:$ref_dir/starindex/hg38index
        hg19:$ref_dir/starindex/hg19index
    fasta:
        hg38:$ref_dir/hg38/hg38.fa
        hg19:$ref_dir/hg19/hg19.fa

    gtf:
        hg38:$ref_dir/hg38/gencode.v30.annotation.gtf
        hg19:$ref_dir/hg19/gencode.v19.annotation.gtf

#directory for input and output files
datadir:
    samples:$RNA_Seqdir/samples.txt
    fastq: $RNA_Seqdir/demo_data
    bam: $RNA_Seqdir/bam
    quant:$RNA_Seqdir/quant